Structure based drug design traditionally has relied on the availability of high resolution x-ray crystallographic structures of the protein target of interest. Given our interest in protein structure prediction and in the conformation of loops, and given the co-existence of a structure-based anti-parasitic drug design program that was stalled owing to particular difficulties with obtaining sufficiently pure malaria trophozoite cysteine protease and schistosome cercarial elastase for crystallographic studies, we constructed models of these two enzymes based on their homology to cysteine and serine proteases of known structure. This work led to the identification of two small molecules: Oxalic bis 2 hydroxy-1-naphthyl methylene hydrazide, a malaria trophozoite cysteine protease inhibitor that was active against the intact parasite (IC50 value = 7mM); and 2-4 methoxybenzoyl 1-naphthoic acid, a cercarial elastase inhibitor (Ki=3mM) that inhibited parasite migration through skin. Analog design was based on the putative configurations of a ligand docked to a model of the three-dimensional structure of a malarial cysteine protease constructed by homology with papain and actinidin. In the absence of a crystal structure of the enzyme or enzyme-inhibitor complex, the ability to make and test quickly a wide variety of compounds was instrumental in our effort to build a structure-activity profile for inhibitor design. The hallmark of this method was simplified chemistry using commercially available starting materials. Beginning with oxalic bis (2-hydroxy-1-naphthylmethylene) hydrazide, an inhibitor identified in a computational screen of the protease model against a database of small molecules, and following our design/synthesis strategy, we have obtained increasingly potent derivatives that block the ability of the parasites to infect and/or mature in red blood cells. These compounds represent a new class of anti-malarial chemotherapeutics that were identified from a computational search based on a model of the target trophozoite cysteine protease. Increasingly potent compounds have been identified through an intimate collaboration between computational and synthetic chemists in the absence of a detailed experimental structure of the target enzyme. These compounds approach the activity of chloroquine (IC50 = 20nM), but have a distinctly different mechanism of action. We have now shown that these compounds are active against chloroquine-resistant malaria. We are applying this approach to several other drug design targets including Hepatitis A 3C proteinase, a cysteine protease from T. Cruzi, prostate specific antigen and a dihydrofolate reductase from cryptosporidium. In an effort to understand the properties of malaria cysteine proteases from other species that cause human disease, we have studied the sequence and probable structure of the Plasmodium vivax protease recently cloned by our collaborator, Phil Rosenthal. We were able to show that while the cysteine proteases from various malaria species vary, the residues that line the subsite specificity pockets change little thereby preserving their hemoglobinase function in contrast to other cysteine proteases with similar degrees of sequence conservation but distinct functions.